josh
February 14, 2023, 10:52am
1
GROMACS version: 2021.5
Hi all,
I am using amber parameters and have prep and frcmod files for ATP, how would I convert these to rtp files? I tried using acpype, but I would then require mol2 or pdb files, would i have to convert prep and frcmod files to pdb / mol2 first and if so, where would I do that?
I am also using carlson’s modified phosphate parameters and converted the units and such and placed them within the ffnonbonded, bonded.itp and “O3” in the atomtypes files. I converted the dihedral types from kcal to kj and using func 9 such as below. I’m not sure if the negative values from AMBER can also be used in the gromacs form.
O2 P OS CT 9 0.0 -1.56000 -3 ; meagher
I’ve also seen a thread to use http://bugzilla.gromacs.org/issues/721 but unfortunately the link is dead.
Also to note im using the atp.pdb from charmm gui small molecule library . Can i still use this for gromacs pdb2gmx?
Teslim
February 15, 2023, 4:39pm
2
Try acpype. See original paper here
josh
February 16, 2023, 3:38pm
3
Would this be used for the atp.prep file? or would I use a ATP smiles file / ATP pdb from charmm?
Teslim
February 16, 2023, 4:19pm
4
Use Antechamber (http://ambermd.org/antechamber/ac.html#antechamber ) to convert the prepi file to mol2 and then, use acpype to create gromacs files from the created mol2.
satti
June 7, 2023, 2:30pm
5
Hello Josh,
Were you able to generate the ATP forcefield from AMBER. Would you kindly share the topology?
josh
June 7, 2023, 2:47pm
6
; atp_GMX.itp created by acpype (v: 2022.6.6) on Tue Feb 21 09:07:01 2023
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon Amb
O2 O2 0.00000 0.00000 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100
P P 0.00000 0.00000 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000
OS OS 0.00000 0.00000 A 3.00001e-01 7.11280e-01 ; 1.68 0.1700
CT CT 0.00000 0.00000 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094
H1 H1 0.00000 0.00000 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157
H2 H2 0.00000 0.00000 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157
N* N* 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
CK CK 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
H5 H5 0.00000 0.00000 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150
NB NB 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
CB CB 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
CA CA 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
N2 N2 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
H H 0.00000 0.00000 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157
NC NC 0.00000 0.00000 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700
CQ CQ 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860
OH OH 0.00000 0.00000 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104
HO HO 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000
[ moleculetype ]
;name nrexcl
atp 3
[ atoms ]
; nr type resi res atom cgnr charge mass ; qtot bond_type
1 O2 1 atp O1G 1 -0.782167 16.00000 ; qtot -0.782
2 P 1 atp PG 2 1.514900 30.97000 ; qtot 0.733
3 O2 1 atp O2G 3 -0.782167 16.00000 ; qtot -0.049
4 O2 1 atp O3G 4 -0.782167 16.00000 ; qtot -0.832
5 OS 1 atp O3B 5 -0.840800 16.00000 ; qtot -1.672
6 P 1 atp PB 6 1.751801 30.97000 ; qtot 0.079
7 O2 1 atp O1B 7 -0.921000 16.00000 ; qtot -0.842
8 O2 1 atp O2B 8 -0.921000 16.00000 ; qtot -1.763
9 OS 1 atp O3A 9 -0.828800 16.00000 ; qtot -2.591
10 P 1 atp PA 10 1.602800 30.97000 ; qtot -0.989
11 O2 1 atp O1A 11 -0.895000 16.00000 ; qtot -1.884
12 O2 1 atp O2A 12 -0.895000 16.00000 ; qtot -2.779
13 OS 1 atp O5* 13 -0.592200 16.00000 ; qtot -3.371
14 CT 1 atp C5* 14 0.194400 12.01000 ; qtot -3.176
15 H1 1 atp H50 15 0.029200 1.00800 ; qtot -3.147
16 H1 1 atp H51 16 0.029200 1.00800 ; qtot -3.118
17 CT 1 atp C4* 17 0.081100 12.01000 ; qtot -3.037
18 H1 1 atp H40 18 0.071700 1.00800 ; qtot -2.965
19 OS 1 atp O4* 19 -0.440600 16.00000 ; qtot -3.406
20 CT 1 atp C1* 20 0.241800 12.01000 ; qtot -3.164
21 H2 1 atp H10 21 0.044700 1.00800 ; qtot -3.119
22 N* 1 atp N9 22 -0.275000 14.01000 ; qtot -3.394
23 CK 1 atp C8 23 0.346700 12.01000 ; qtot -3.048
24 H5 1 atp H80 24 0.103800 1.00800 ; qtot -2.944
25 NB 1 atp N7 25 -0.775100 14.01000 ; qtot -3.719
26 CB 1 atp C5 26 -0.110200 12.01000 ; qtot -3.829
27 CA 1 atp C6 27 0.524200 12.01000 ; qtot -3.305
28 N2 1 atp N6 28 -0.890500 14.01000 ; qtot -4.195
29 H 1 atp H60 29 0.348800 1.00800 ; qtot -3.847
30 H 1 atp H61 30 0.348800 1.00800 ; qtot -3.498
31 NC 1 atp N1 31 -0.781000 14.01000 ; qtot -4.279
32 CQ 1 atp C2 32 0.554900 12.01000 ; qtot -3.724
33 H5 1 atp H2 33 -0.003900 1.00800 ; qtot -3.728
34 NC 1 atp N3 34 -0.706000 14.01000 ; qtot -4.434
35 CB 1 atp C4 35 0.386800 12.01000 ; qtot -4.047
36 CT 1 atp C3* 36 0.114100 12.01000 ; qtot -3.933
37 H1 1 atp H30 37 0.084700 1.00800 ; qtot -3.848
38 OH 1 atp O3* 38 -0.678800 16.00000 ; qtot -4.527
39 HO 1 atp H3' 39 0.511000 1.00800 ; qtot -4.016
40 CT 1 atp C2* 40 0.115100 12.01000 ; qtot -3.901
41 H1 1 atp H20 41 0.104700 1.00800 ; qtot -3.796
42 OH 1 atp O2* 42 -0.619800 16.00000 ; qtot -4.416
43 HO 1 atp H2' 43 0.416000 1.00800 ; qtot -4.000
[ bonds ]
; ai aj funct r k
1 2 1 1.4800e-01 4.3932e+05 ; O1G - PG
2 3 1 1.4800e-01 4.3932e+05 ; PG - O2G
2 4 1 1.4800e-01 4.3932e+05 ; PG - O3G
2 5 1 1.6100e-01 1.9246e+05 ; PG - O3B
5 6 1 1.6100e-01 1.9246e+05 ; O3B - PB
6 7 1 1.4800e-01 4.3932e+05 ; PB - O1B
6 8 1 1.4800e-01 4.3932e+05 ; PB - O2B
6 9 1 1.6100e-01 1.9246e+05 ; PB - O3A
9 10 1 1.6100e-01 1.9246e+05 ; O3A - PA
10 11 1 1.4800e-01 4.3932e+05 ; PA - O1A
10 12 1 1.4800e-01 4.3932e+05 ; PA - O2A
10 13 1 1.6100e-01 1.9246e+05 ; PA - O5*
13 14 1 1.4100e-01 2.6778e+05 ; O5* - C5*
14 15 1 1.0900e-01 2.8451e+05 ; C5* - H50
14 16 1 1.0900e-01 2.8451e+05 ; C5* - H51
14 17 1 1.5260e-01 2.5941e+05 ; C5* - C4*
17 18 1 1.0900e-01 2.8451e+05 ; C4* - H40
17 19 1 1.4100e-01 2.6778e+05 ; C4* - O4*
17 36 1 1.5260e-01 2.5941e+05 ; C4* - C3*
19 20 1 1.4100e-01 2.6778e+05 ; O4* - C1*
20 21 1 1.0900e-01 2.8451e+05 ; C1* - H10
20 22 1 1.4750e-01 2.8200e+05 ; C1* - N9
20 40 1 1.5260e-01 2.5941e+05 ; C1* - C2*
22 23 1 1.3710e-01 3.6819e+05 ; N9 - C8
22 35 1 1.3740e-01 3.6484e+05 ; N9 - C4
23 24 1 1.0800e-01 3.0711e+05 ; C8 - H80
23 25 1 1.3040e-01 4.4267e+05 ; C8 - N7
25 26 1 1.3910e-01 3.4644e+05 ; N7 - C5
26 27 1 1.4040e-01 3.9246e+05 ; C5 - C6
26 35 1 1.3700e-01 4.3514e+05 ; C5 - C4
27 28 1 1.3400e-01 4.0250e+05 ; C6 - N6
27 31 1 1.3390e-01 4.0417e+05 ; C6 - N1
28 29 1 1.0100e-01 3.6317e+05 ; N6 - H60
28 30 1 1.0100e-01 3.6317e+05 ; N6 - H61
31 32 1 1.3240e-01 4.2007e+05 ; N1 - C2
32 33 1 1.0800e-01 3.0711e+05 ; C2 - H2
32 34 1 1.3240e-01 4.2007e+05 ; C2 - N3
34 35 1 1.3540e-01 3.8576e+05 ; N3 - C4
36 37 1 1.0900e-01 2.8451e+05 ; C3* - H30
36 38 1 1.4100e-01 2.6778e+05 ; C3* - O3*
36 40 1 1.5260e-01 2.5941e+05 ; C3* - C2*
38 39 1 9.6000e-02 4.6275e+05 ; O3* - H3'
40 41 1 1.0900e-01 2.8451e+05 ; C2* - H20
40 42 1 1.4100e-01 2.6778e+05 ; C2* - O2*
42 43 1 9.6000e-02 4.6275e+05 ; O2* - H2'
[ pairs ]
; ai aj funct
1 6 1 ; O1G - PB
2 7 1 ; PG - O1B
2 8 1 ; PG - O2B
2 9 1 ; PG - O3A
3 6 1 ; O2G - PB
4 6 1 ; O3G - PB
5 10 1 ; O3B - PA
6 11 1 ; PB - O1A
6 12 1 ; PB - O2A
6 13 1 ; PB - O5*
7 10 1 ; O1B - PA
8 10 1 ; O2B - PA
9 14 1 ; O3A - C5*
10 15 1 ; PA - H50
10 16 1 ; PA - H51
10 17 1 ; PA - C4*
11 14 1 ; O1A - C5*
12 14 1 ; O2A - C5*
13 18 1 ; O5* - H40
13 19 1 ; O5* - O4*
13 36 1 ; O5* - C3*
14 20 1 ; C5* - C1*
14 37 1 ; C5* - H30
14 38 1 ; C5* - O3*
14 40 1 ; C5* - C2*
15 18 1 ; H50 - H40
15 19 1 ; H50 - O4*
15 36 1 ; H50 - C3*
16 18 1 ; H51 - H40
16 19 1 ; H51 - O4*
16 36 1 ; H51 - C3*
17 21 1 ; C4* - H10
17 22 1 ; C4* - N9
17 39 1 ; C4* - H3'
17 41 1 ; C4* - H20
17 42 1 ; C4* - O2*
18 20 1 ; H40 - C1*
18 37 1 ; H40 - H30
18 38 1 ; H40 - O3*
18 40 1 ; H40 - C2*
19 23 1 ; O4* - C8
19 35 1 ; O4* - C4
19 37 1 ; O4* - H30
19 38 1 ; O4* - O3*
19 41 1 ; O4* - H20
19 42 1 ; O4* - O2*
20 24 1 ; C1* - H80
20 25 1 ; C1* - N7
20 26 1 ; C1* - C5
20 34 1 ; C1* - N3
20 37 1 ; C1* - H30
20 38 1 ; C1* - O3*
20 43 1 ; C1* - H2'
21 23 1 ; H10 - C8
21 35 1 ; H10 - C4
21 36 1 ; H10 - C3*
21 41 1 ; H10 - H20
21 42 1 ; H10 - O2*
22 27 1 ; N9 - C6
22 32 1 ; N9 - C2
22 36 1 ; N9 - C3*
22 41 1 ; N9 - H20
22 42 1 ; N9 - O2*
23 27 1 ; C8 - C6
23 34 1 ; C8 - N3
23 40 1 ; C8 - C2*
24 26 1 ; H80 - C5
24 35 1 ; H80 - C4
25 28 1 ; N7 - N6
25 31 1 ; N7 - N1
25 34 1 ; N7 - N3
26 29 1 ; C5 - H60
26 30 1 ; C5 - H61
26 32 1 ; C5 - C2
27 33 1 ; C6 - H2
27 34 1 ; C6 - N3
28 32 1 ; N6 - C2
28 35 1 ; N6 - C4
29 31 1 ; H60 - N1
30 31 1 ; H61 - N1
31 35 1 ; N1 - C4
33 35 1 ; H2 - C4
35 40 1 ; C4 - C2*
36 43 1 ; C3* - H2'
37 39 1 ; H30 - H3'
37 41 1 ; H30 - H20
37 42 1 ; H30 - O2*
38 41 1 ; O3* - H20
38 42 1 ; O3* - O2*
39 40 1 ; H3' - C2*
41 43 1 ; H20 - H2'
[ angles ]
; ai aj ak funct theta cth
1 2 3 1 1.1990e+02 1.1715e+03 ; O1G - PG - O2G
1 2 4 1 1.1990e+02 1.1715e+03 ; O1G - PG - O3G
1 2 5 1 1.0823e+02 8.3680e+02 ; O1G - PG - O3B
2 5 6 1 1.2050e+02 8.3680e+02 ; PG - O3B - PB
3 2 4 1 1.1990e+02 1.1715e+03 ; O2G - PG - O3G
3 2 5 1 1.0823e+02 8.3680e+02 ; O2G - PG - O3B
4 2 5 1 1.0823e+02 8.3680e+02 ; O3G - PG - O3B
5 6 7 1 1.0823e+02 8.3680e+02 ; O3B - PB - O1B
5 6 8 1 1.0823e+02 8.3680e+02 ; O3B - PB - O2B
5 6 9 1 1.0260e+02 3.7656e+02 ; O3B - PB - O3A
6 9 10 1 1.2050e+02 8.3680e+02 ; PB - O3A - PA
7 6 8 1 1.1990e+02 1.1715e+03 ; O1B - PB - O2B
7 6 9 1 1.0823e+02 8.3680e+02 ; O1B - PB - O3A
8 6 9 1 1.0823e+02 8.3680e+02 ; O2B - PB - O3A
9 10 11 1 1.0823e+02 8.3680e+02 ; O3A - PA - O1A
9 10 12 1 1.0823e+02 8.3680e+02 ; O3A - PA - O2A
9 10 13 1 1.0260e+02 3.7656e+02 ; O3A - PA - O5*
10 13 14 1 1.2050e+02 8.3680e+02 ; PA - O5* - C5*
11 10 12 1 1.1990e+02 1.1715e+03 ; O1A - PA - O2A
11 10 13 1 1.0823e+02 8.3680e+02 ; O1A - PA - O5*
12 10 13 1 1.0823e+02 8.3680e+02 ; O2A - PA - O5*
13 14 15 1 1.0950e+02 4.1840e+02 ; O5* - C5* - H50
13 14 16 1 1.0950e+02 4.1840e+02 ; O5* - C5* - H51
13 14 17 1 1.0950e+02 4.1840e+02 ; O5* - C5* - C4*
14 17 18 1 1.0950e+02 4.1840e+02 ; C5* - C4* - H40
14 17 19 1 1.0950e+02 4.1840e+02 ; C5* - C4* - O4*
14 17 36 1 1.0950e+02 3.3472e+02 ; C5* - C4* - C3*
15 14 16 1 1.0950e+02 2.9288e+02 ; H50 - C5* - H51
15 14 17 1 1.0950e+02 4.1840e+02 ; H50 - C5* - C4*
16 14 17 1 1.0950e+02 4.1840e+02 ; H51 - C5* - C4*
17 19 20 1 1.0950e+02 5.0208e+02 ; C4* - O4* - C1*
17 36 37 1 1.0950e+02 4.1840e+02 ; C4* - C3* - H30
17 36 38 1 1.0950e+02 4.1840e+02 ; C4* - C3* - O3*
17 36 40 1 1.0950e+02 3.3472e+02 ; C4* - C3* - C2*
18 17 19 1 1.0950e+02 4.1840e+02 ; H40 - C4* - O4*
18 17 36 1 1.0950e+02 4.1840e+02 ; H40 - C4* - C3*
19 17 36 1 1.0950e+02 4.1840e+02 ; O4* - C4* - C3*
19 20 21 1 1.0950e+02 4.1840e+02 ; O4* - C1* - H10
19 20 22 1 1.0950e+02 4.1840e+02 ; O4* - C1* - N9
19 20 40 1 1.0950e+02 4.1840e+02 ; O4* - C1* - C2*
20 22 23 1 1.2880e+02 5.8576e+02 ; C1* - N9 - C8
20 22 35 1 1.2580e+02 5.8576e+02 ; C1* - N9 - C4
20 40 36 1 1.0950e+02 3.3472e+02 ; C1* - C2* - C3*
20 40 41 1 1.0950e+02 4.1840e+02 ; C1* - C2* - H20
20 40 42 1 1.0950e+02 4.1840e+02 ; C1* - C2* - O2*
21 20 22 1 1.0950e+02 4.1840e+02 ; H10 - C1* - N9
21 20 40 1 1.0950e+02 4.1840e+02 ; H10 - C1* - C2*
22 20 40 1 1.0950e+02 4.1840e+02 ; N9 - C1* - C2*
22 23 24 1 1.2305e+02 4.1840e+02 ; N9 - C8 - H80
22 23 25 1 1.1390e+02 5.8576e+02 ; N9 - C8 - N7
22 35 26 1 1.0620e+02 5.8576e+02 ; N9 - C4 - C5
22 35 34 1 1.2620e+02 5.8576e+02 ; N9 - C4 - N3
23 22 35 1 1.0540e+02 5.8576e+02 ; C8 - N9 - C4
23 25 26 1 1.0380e+02 5.8576e+02 ; C8 - N7 - C5
24 23 25 1 1.2305e+02 4.1840e+02 ; H80 - C8 - N7
25 26 27 1 1.3240e+02 5.8576e+02 ; N7 - C5 - C6
25 26 35 1 1.1040e+02 5.8576e+02 ; N7 - C5 - C4
26 27 28 1 1.2350e+02 5.8576e+02 ; C5 - C6 - N6
26 27 31 1 1.1730e+02 5.8576e+02 ; C5 - C6 - N1
26 35 34 1 1.2770e+02 5.8576e+02 ; C5 - C4 - N3
27 26 35 1 1.1730e+02 5.2718e+02 ; C6 - C5 - C4
27 28 29 1 1.2000e+02 4.1840e+02 ; C6 - N6 - H60
27 28 30 1 1.2000e+02 4.1840e+02 ; C6 - N6 - H61
27 31 32 1 1.1860e+02 5.8576e+02 ; C6 - N1 - C2
28 27 31 1 1.1930e+02 5.8576e+02 ; N6 - C6 - N1
29 28 30 1 1.2000e+02 2.9288e+02 ; H60 - N6 - H61
31 32 33 1 1.1545e+02 4.1840e+02 ; N1 - C2 - H2
31 32 34 1 1.2910e+02 5.8576e+02 ; N1 - C2 - N3
32 34 35 1 1.1100e+02 5.8576e+02 ; C2 - N3 - C4
33 32 34 1 1.1545e+02 4.1840e+02 ; H2 - C2 - N3
36 38 39 1 1.0850e+02 4.6024e+02 ; C3* - O3* - H3'
36 40 41 1 1.0950e+02 4.1840e+02 ; C3* - C2* - H20
36 40 42 1 1.0950e+02 4.1840e+02 ; C3* - C2* - O2*
37 36 38 1 1.0950e+02 4.1840e+02 ; H30 - C3* - O3*
37 36 40 1 1.0950e+02 4.1840e+02 ; H30 - C3* - C2*
38 36 40 1 1.0950e+02 4.1840e+02 ; O3* - C3* - C2*
40 42 43 1 1.0850e+02 4.6024e+02 ; C2* - O2* - H2'
41 40 42 1 1.0950e+02 4.1840e+02 ; H20 - C2* - O2*
[ dihedrals ] ; propers
; for gromacs 4.5 or higher, using funct 9
; i j k l func phase kd pn
1 2 5 6 9 0.00 1.04600 3 ; O1G- PG- O3B- PB
2 5 6 7 9 0.00 1.04600 3 ; PG- O3B- PB- O1B
2 5 6 8 9 0.00 1.04600 3 ; PG- O3B- PB- O2B
2 5 6 9 9 0.00 1.04600 3 ; PG- O3B- PB- O3A
3 2 5 6 9 0.00 1.04600 3 ; O2G- PG- O3B- PB
4 2 5 6 9 0.00 1.04600 3 ; O3G- PG- O3B- PB
5 6 9 10 9 0.00 1.04600 3 ; O3B- PB- O3A- PA
6 9 10 11 9 0.00 1.04600 3 ; PB- O3A- PA- O1A
6 9 10 12 9 0.00 1.04600 3 ; PB- O3A- PA- O2A
6 9 10 13 9 0.00 1.04600 3 ; PB- O3A- PA- O5*
7 6 9 10 9 0.00 1.04600 3 ; O1B- PB- O3A- PA
8 6 9 10 9 0.00 1.04600 3 ; O2B- PB- O3A- PA
9 10 13 14 9 0.00 1.04600 3 ; O3A- PA- O5*- C5*
9 10 13 14 9 0.00 5.02080 2 ; O3A- PA- O5*- C5*
10 13 14 15 9 0.00 1.60387 3 ; PA- O5*- C5*- H50
10 13 14 16 9 0.00 1.60387 3 ; PA- O5*- C5*- H51
10 13 14 17 9 0.00 1.60387 3 ; PA- O5*- C5*- C4*
10 13 14 17 9 180.00 16.52680 1 ; PA- O5*- C5*- C4*
11 10 13 14 9 0.00 2.30120 3 ; O1A- PA- O5*- C5*
11 10 13 14 9 0.00 3.34720 2 ; O1A- PA- O5*- C5*
12 10 13 14 9 0.00 2.30120 3 ; O2A- PA- O5*- C5*
12 10 13 14 9 0.00 3.34720 2 ; O2A- PA- O5*- C5*
13 14 17 18 9 0.00 0.00000 0 ; O5*- C5*- C4*- H40
13 14 17 18 9 0.00 1.04600 1 ; O5*- C5*- C4*- H40
13 14 17 19 9 0.00 0.60250 3 ; O5*- C5*- C4*- O4*
13 14 17 19 9 0.00 4.91620 2 ; O5*- C5*- C4*- O4*
13 14 17 36 9 0.00 0.65084 3 ; O5*- C5*- C4*- C3*
14 17 19 20 9 0.00 1.60247 3 ; C5*- C4*- O4*- C1*
14 17 19 20 9 180.00 0.41840 2 ; C5*- C4*- O4*- C1*
14 17 36 37 9 0.00 0.65084 3 ; C5*- C4*- C3*- H30
14 17 36 38 9 0.00 0.65084 3 ; C5*- C4*- C3*- O3*
14 17 36 40 9 0.00 0.75312 3 ; C5*- C4*- C3*- C2*
14 17 36 40 9 180.00 0.83680 1 ; C5*- C4*- C3*- C2*
14 17 36 40 9 180.00 1.04600 2 ; C5*- C4*- C3*- C2*
15 14 17 18 9 0.00 0.65084 3 ; H50- C5*- C4*- H40
15 14 17 19 9 0.00 0.00000 0 ; H50- C5*- C4*- O4*
15 14 17 19 9 0.00 1.04600 1 ; H50- C5*- C4*- O4*
15 14 17 36 9 0.00 0.65084 3 ; H50- C5*- C4*- C3*
16 14 17 18 9 0.00 0.65084 3 ; H51- C5*- C4*- H40
16 14 17 19 9 0.00 0.00000 0 ; H51- C5*- C4*- O4*
16 14 17 19 9 0.00 1.04600 1 ; H51- C5*- C4*- O4*
16 14 17 36 9 0.00 0.65084 3 ; H51- C5*- C4*- C3*
17 19 20 21 9 0.00 1.60387 3 ; C4*- O4*- C1*- H10
17 19 20 22 9 0.00 1.60247 3 ; C4*- O4*- C1*- N9
17 19 20 22 9 0.00 2.71960 2 ; C4*- O4*- C1*- N9
17 19 20 40 9 0.00 1.60247 3 ; C4*- O4*- C1*- C2*
17 19 20 40 9 180.00 0.41840 2 ; C4*- O4*- C1*- C2*
17 36 38 39 9 0.00 0.66944 3 ; C4*- C3*- O3*- H3'
17 36 38 39 9 0.00 1.04600 1 ; C4*- C3*- O3*- H3'
17 36 40 20 9 0.00 0.75312 3 ; C4*- C3*- C2*- C1*
17 36 40 20 9 180.00 0.83680 1 ; C4*- C3*- C2*- C1*
17 36 40 20 9 180.00 1.04600 2 ; C4*- C3*- C2*- C1*
17 36 40 41 9 0.00 0.65084 3 ; C4*- C3*- C2*- H20
17 36 40 42 9 0.00 0.65084 3 ; C4*- C3*- C2*- O2*
18 17 19 20 9 0.00 1.60387 3 ; H40- C4*- O4*- C1*
18 17 36 37 9 0.00 0.65084 3 ; H40- C4*- C3*- H30
18 17 36 38 9 0.00 0.00000 0 ; H40- C4*- C3*- O3*
18 17 36 38 9 0.00 1.04600 1 ; H40- C4*- C3*- O3*
18 17 36 40 9 0.00 0.65084 3 ; H40- C4*- C3*- C2*
19 17 36 37 9 0.00 0.00000 0 ; O4*- C4*- C3*- H30
19 17 36 37 9 0.00 1.04600 1 ; O4*- C4*- C3*- H30
19 17 36 38 9 0.00 0.60250 3 ; O4*- C4*- C3*- O3*
19 17 36 38 9 0.00 4.91620 2 ; O4*- C4*- C3*- O3*
19 17 36 40 9 0.00 0.65084 3 ; O4*- C4*- C3*- C2*
19 20 22 23 9 0.00 0.00000 0 ; O4*- C1*- N9- C8
19 20 22 23 9 0.00 10.46000 1 ; O4*- C1*- N9- C8
19 20 22 35 9 0.00 0.00000 0 ; O4*- C1*- N9- C4
19 20 40 36 9 0.00 0.65084 3 ; O4*- C1*- C2*- C3*
19 20 40 41 9 0.00 0.00000 0 ; O4*- C1*- C2*- H20
19 20 40 41 9 0.00 1.04600 1 ; O4*- C1*- C2*- H20
19 20 40 42 9 0.00 0.60250 3 ; O4*- C1*- C2*- O2*
19 20 40 42 9 0.00 4.91620 2 ; O4*- C1*- C2*- O2*
20 19 17 36 9 0.00 1.60247 3 ; C1*- O4*- C4*- C3*
20 19 17 36 9 180.00 0.41840 2 ; C1*- O4*- C4*- C3*
20 22 23 24 9 180.00 7.11280 2 ; C1*- N9- C8- H80
20 22 23 25 9 180.00 7.11280 2 ; C1*- N9- C8- N7
20 22 35 26 9 180.00 6.90360 2 ; C1*- N9- C4- C5
20 22 35 34 9 180.00 6.90360 2 ; C1*- N9- C4- N3
20 40 36 37 9 0.00 0.65084 3 ; C1*- C2*- C3*- H30
20 40 36 38 9 0.00 0.65084 3 ; C1*- C2*- C3*- O3*
20 40 42 43 9 0.00 0.66944 3 ; C1*- C2*- O2*- H2'
20 40 42 43 9 0.00 1.04600 1 ; C1*- C2*- O2*- H2'
21 20 22 23 9 0.00 0.00000 0 ; H10- C1*- N9- C8
21 20 22 35 9 0.00 0.00000 0 ; H10- C1*- N9- C4
21 20 40 36 9 0.00 0.65084 3 ; H10- C1*- C2*- C3*
21 20 40 41 9 0.00 0.65084 3 ; H10- C1*- C2*- H20
21 20 40 42 9 0.00 0.65084 3 ; H10- C1*- C2*- O2*
22 20 40 36 9 0.00 0.65084 3 ; N9- C1*- C2*- C3*
22 20 40 41 9 0.00 0.65084 3 ; N9- C1*- C2*- H20
22 20 40 42 9 0.00 0.65084 3 ; N9- C1*- C2*- O2*
22 23 25 26 9 180.00 41.84000 2 ; N9- C8- N7- C5
22 35 26 25 9 180.00 22.80280 2 ; N9- C4- C5- N7
22 35 26 27 9 180.00 22.80280 2 ; N9- C4- C5- C6
22 35 34 32 9 180.00 17.36360 2 ; N9- C4- N3- C2
23 22 20 40 9 0.00 0.00000 0 ; C8- N9- C1*- C2*
23 22 35 26 9 180.00 6.90360 2 ; C8- N9- C4- C5
23 22 35 34 9 180.00 6.90360 2 ; C8- N9- C4- N3
23 25 26 27 9 180.00 10.66920 2 ; C8- N7- C5- C6
23 25 26 35 9 180.00 10.66920 2 ; C8- N7- C5- C4
24 23 22 35 9 180.00 7.11280 2 ; H80- C8- N9- C4
24 23 25 26 9 180.00 41.84000 2 ; H80- C8- N7- C5
25 23 22 35 9 180.00 7.11280 2 ; N7- C8- N9- C4
25 26 27 28 9 180.00 14.64400 2 ; N7- C5- C6- N6
25 26 27 31 9 180.00 14.64400 2 ; N7- C5- C6- N1
25 26 35 34 9 180.00 22.80280 2 ; N7- C5- C4- N3
26 27 28 29 9 180.00 10.04160 2 ; C5- C6- N6- H60
26 27 28 30 9 180.00 10.04160 2 ; C5- C6- N6- H61
26 27 31 32 9 180.00 20.08320 2 ; C5- C6- N1- C2
26 35 34 32 9 180.00 17.36360 2 ; C5- C4- N3- C2
27 26 35 34 9 180.00 22.80280 2 ; C6- C5- C4- N3
27 31 32 33 9 180.00 28.45120 2 ; C6- N1- C2- H2
27 31 32 34 9 180.00 28.45120 2 ; C6- N1- C2- N3
28 27 26 35 9 180.00 14.64400 2 ; N6- C6- C5- C4
28 27 31 32 9 180.00 20.08320 2 ; N6- C6- N1- C2
29 28 27 31 9 180.00 10.04160 2 ; H60- N6- C6- N1
30 28 27 31 9 180.00 10.04160 2 ; H61- N6- C6- N1
31 27 26 35 9 180.00 14.64400 2 ; N1- C6- C5- C4
31 32 34 35 9 180.00 28.45120 2 ; N1- C2- N3- C4
33 32 34 35 9 180.00 28.45120 2 ; H2- C2- N3- C4
35 22 20 40 9 0.00 0.00000 0 ; C4- N9- C1*- C2*
36 40 42 43 9 0.00 0.66944 3 ; C3*- C2*- O2*- H2'
36 40 42 43 9 0.00 1.04600 1 ; C3*- C2*- O2*- H2'
37 36 38 39 9 0.00 0.69733 3 ; H30- C3*- O3*- H3'
37 36 40 41 9 0.00 0.65084 3 ; H30- C3*- C2*- H20
37 36 40 42 9 0.00 0.00000 0 ; H30- C3*- C2*- O2*
37 36 40 42 9 0.00 1.04600 1 ; H30- C3*- C2*- O2*
38 36 40 41 9 0.00 0.00000 0 ; O3*- C3*- C2*- H20
38 36 40 41 9 0.00 1.04600 1 ; O3*- C3*- C2*- H20
38 36 40 42 9 0.00 0.60250 3 ; O3*- C3*- C2*- O2*
38 36 40 42 9 0.00 4.91620 2 ; O3*- C3*- C2*- O2*
39 38 36 40 9 0.00 0.66944 3 ; H3'- O3*- C3*- C2*
39 38 36 40 9 0.00 1.04600 1 ; H3'- O3*- C3*- C2*
41 40 42 43 9 0.00 0.69733 3 ; H20- C2*- O2*- H2'
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
22 26 35 34 4 180.00 0.00000 2 ; N9- C5- C4- N3
24 22 23 25 4 180.00 4.60240 2 ; H80- N9- C8- N7
25 27 26 35 4 180.00 0.00000 2 ; N7- C6- C5- C4
26 28 27 31 4 180.00 4.60240 2 ; C5- N6- C6- N1
27 29 28 30 4 180.00 4.18400 2 ; C6- H60- N6- H61
33 31 32 34 4 180.00 4.60240 2 ; H2- N1- C2- N3
35 23 22 20 4 180.00 4.18400 2 ; C4- C8- N9- C1*
satti
June 7, 2023, 2:57pm
7
HI Josh,
Thanks a lot. So this topology goes with amber99sb-star-ildn.ff forcefield for Protein? Just to be sure.
regards,
Bijaya
June 3, 2024, 10:12am
8
Dear Josh,http://amber.manchester.ac.uk/ to mol2. But when I visualized the structure, its unphysical. Can you help me with the same , where i might have gone wrong?
Hi Bijaya,
Have you found a solution to your problem? I’m struggling with the exact same issue.